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An elaborate dual-triangle optical path design is applied to share one detector for both alignment and view.
For both alignment programs, gap opening and extension parameters were set to their defaults.
The figures for both alignment lengths are similar and present the same trends (slightly better for 600 bp for all methods, as expected), so we let the results on 300 bp for the Additional file 1.
Similar(57)
For both alignments the minimum length of a block was 10 and gapped positions were included.
To evaluate the quality of new alignments of SVRs over the previous alignments, scores were computed for both alignments.
Variable and parsimoniously informative sites were determined for both alignments.
For a true R500 IMB211 polymorphism, the majority of reads should match the appropriate allele for both alignments.
Standard sequence logos are identical for both alignments; however, CodonLogo is able to discriminate between the two situations.
For both alignments (mtDNA1, mtDNA2; for details about alignments see Methods), we observed a major shift in nucleotide composition between colobine and non-colobine representatives (Additional file 4).
For both alignments we used a threshold α value of 0.001, a random sampling of 100000, and a bootstrap value of 100.
Likelihood mapping, implemented in TREE-PUZZLE to inspect the phylogenetic signal of the alignment (Additional file 2: Table S2), showed a relevant value for both alignments that was slightly reduced when rodents and tree shrew were included.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com